I haven’t seen the comment, but...I don’t view this as a free speech issue, while generally being fairly close to a free-speech absolutist myself.
The reason is that comments are ephemeral by design. And one that is rude is going to be addressed to a particular person, which makes it obsolete and useless as soon as it has been read. If I call you a great poopy head, you know I don’t like you, but that doesn’t really help anyone else who is reading the question/answer. Likewise if I say thanks, that was tremendously helpful and you are an awesome person.
Unless the comment addressed a problem with your answer in a useful manner, it should be deleted.
If the comment is useful, it can be upvoted which will make it slightly less likely to be deleted.